Variant report

Variant	rs10774872
Chromosome Location	chr12:116985895-116985896
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:116985800-116985950	GM12873	blood:	n/a	n/a
2	CUX1	chr12:116985882-116986093	K562	blood:	n/a	n/a
3	POLR2A	chr12:116985620-116986670	GM12892	blood:	n/a	n/a
4	EP300	chr12:116985720-116986082	K562	blood:	n/a	chr12:116985752-116985766 chr12:116985740-116985754 chr12:116985742-116985756
5	RCOR1	chr12:116985726-116986110	K562	blood:	n/a	n/a
6	MAX	chr12:116985311-116986027	K562	blood:	n/a	n/a
7	RUNX3	chr12:116985661-116986372	GM12878	blood:	n/a	n/a
8	BHLHE40	chr12:116985492-116986143	K562	blood:	n/a	n/a
9	NFIC	chr12:116985581-116986289	GM12878	blood:	n/a	n/a
10	TEAD4	chr12:116985591-116986242	K562	blood:	n/a	n/a
11	BHLHE40	chr12:116985825-116986184	GM12878	blood:	n/a	n/a
12	BCL11A	chr12:116985778-116986081	GM12878	blood:	n/a	n/a
13	REST	chr12:116985806-116986258	PFSK-1	brain:	n/a	chr12:116985984-116985991
14	BCL11A	chr12:116985792-116986079	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:116985709-116986249	GM12892	blood:	n/a	n/a
16	SMC3	chr12:116985881-116986125	GM12878	blood:	n/a	chr12:116985938-116985946
17	STAT3	chr12:116985802-116985976	MCF10A-Er-Src	breast:	n/a	n/a
18	SPI1	chr12:116985611-116986166	HL-60	blood:	n/a	chr12:116985859-116985872
19	EP300	chr12:116985893-116986118	GM12878	blood:	n/a	n/a
20	SPI1	chr12:116985753-116986052	GM12878	blood:	n/a	chr12:116985859-116985872
21	PML	chr12:116985669-116986292	GM12878	blood:	n/a	n/a
22	IKZF1	chr12:116985594-116986298	GM12878	blood:	n/a	n/a
23	SIN3AK20	chr12:116985825-116986155	PFSK-1	brain:	n/a	n/a
24	PBX3	chr12:116985760-116985967	GM12878	blood:	n/a	n/a
25	MAX	chr12:116985683-116986477	NB4	blood:	n/a	n/a
26	POLR2A	chr12:116985763-116986323	PFSK-1	brain:	n/a	n/a
27	MAZ	chr12:116985432-116986083	K562	blood:	n/a	n/a
28	CCNT2	chr12:116985891-116986123	K562	blood:	n/a	n/a
29	EBF1	chr12:116985775-116986084	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:116985716-116986252	HL-60	blood:	n/a	n/a
31	MAFK	chr12:116985657-116986035	K562	blood:	n/a	n/a
32	RELA	chr12:116985733-116986487	GM19099	blood:	n/a	n/a
33	REST	chr12:116985778-116986221	PFSK-1	brain:	n/a	chr12:116985984-116985991
34	PAX5	chr12:116985863-116986158	GM12878	blood:	n/a	n/a
35	TBL1XR1	chr12:116985771-116986109	GM12878	blood:	n/a	n/a
36	PAX5	chr12:116985642-116986193	GM12878	blood:	n/a	n/a
37	JUND	chr12:116985434-116986113	K562	blood:	n/a	n/a
38	RUNX3	chr12:116985697-116986232	GM12878	blood:	n/a	n/a
39	FOXM1	chr12:116985646-116986234	GM12878	blood:	n/a	n/a
40	RCOR1	chr12:116985799-116986124	K562	blood:	n/a	n/a
41	MYC	chr12:116985596-116986320	NB4	blood:	n/a	n/a
42	POLR2A	chr12:116985759-116986607	GM12892	blood:	n/a	n/a
43	TCF12	chr12:116985771-116986141	GM12878	blood:	n/a	n/a
44	EP300	chr12:116985701-116986210	GM12878	blood:	n/a	chr12:116985752-116985766 chr12:116985740-116985754 chr12:116985742-116985756
45	ZNF384	chr12:116985550-116985973	K562	blood:	n/a	n/a
46	NFATC1	chr12:116985654-116986196	GM12878	blood:	n/a	n/a
47	TAF1	chr12:116985861-116986162	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr12:116985583-116986285	HL-60	blood:	n/a	n/a
49	FOXP2	chr12:116985848-116986171	PFSK-1	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP1LC3B2-1	chr12:116985551-116986093	XLOC_009898

Variant related genes	Relation type
ENSG00000258102	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10774871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10850662	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10850663	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068062	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068070	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11068072	0.86[AMR][1000 genomes]
rs11068075	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11609040	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11609872	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11610226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615960	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1394801	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394802	0.82[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047952	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2089222	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2102294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893685	0.86[ASN][1000 genomes]
rs60521218	0.95[ASN][1000 genomes]
rs6490075	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6490076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297552	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300418	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304300	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315385	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954181	0.89[ASN][1000 genomes]
rs7961538	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7969190	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969566	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7972701	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7976256	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116973000-116986000	Weak transcription	Aorta	Aorta
2	chr12:116978200-116989400	Weak transcription	Esophagus	oesophagus
3	chr12:116981600-116986000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:116982000-116986000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:116982400-116986000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:116983200-116986800	Enhancers	K562	blood
7	chr12:116983600-116986000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:116983800-116986200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:116984200-116986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:116984200-116996800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:116984200-116997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:116984800-116986800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:116984800-116986800	Enhancers	Fetal Muscle Leg	muscle
14	chr12:116985000-116986000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr12:116985000-116986000	Enhancers	Primary B cells from cord blood	blood
16	chr12:116985000-116986000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:116985000-116986800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr12:116985000-116987000	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:116985200-116986000	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:116985200-116986000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:116985200-116986400	Enhancers	Fetal Muscle Trunk	muscle
22	chr12:116985200-116986600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:116985200-116986600	Enhancers	Fetal Brain Male	brain
24	chr12:116985400-116986000	Enhancers	Fetal Heart	heart
25	chr12:116985400-116986400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:116985400-116986400	Enhancers	Placenta	Placenta
27	chr12:116985400-116986600	Enhancers	Colon Smooth Muscle	Colon
28	chr12:116985400-116986800	Enhancers	Fetal Thymus	thymus
29	chr12:116985400-116986800	Enhancers	Spleen	Spleen
30	chr12:116985600-116986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:116985600-116986200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr12:116985600-116986400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr12:116985600-116986400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr12:116985600-116986600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:116985600-116986600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:116985600-116986600	Enhancers	Adipose Nuclei	Adipose
37	chr12:116985600-116986600	Enhancers	Fetal Brain Female	brain
38	chr12:116985600-116986600	Enhancers	Fetal Stomach	stomach
39	chr12:116985600-116986600	Enhancers	HSMMtube	muscle
40	chr12:116985800-116986000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:116985800-116986000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:116985800-116986200	Enhancers	Primary T cells from cord blood	blood
43	chr12:116985800-116986200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:116985800-116986200	Flanking Active TSS	GM12878-XiMat	blood
45	chr12:116985800-116986400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr12:116985800-116986600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr12:116985800-116986600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:116985800-116986600	Enhancers	Fetal Lung	lung
49	chr12:116985800-116986600	Enhancers	Lung	lung
50	chr12:116985800-116986600	Enhancers	Psoas Muscle	Psoas

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